Matt:LabNotes/2015-4-27: Difference between revisions

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>Mzcai
>Mzcai
Line 9: Line 9:
**[[Media:OutputFile_0gap_final.full_info.V7.txt|OutputFile_0gap_final.full_info.V7.txt]] > CA12k_Nov2014_V7.bed
**[[Media:OutputFile_0gap_final.full_info.V7.txt|OutputFile_0gap_final.full_info.V7.txt]] > CA12k_Nov2014_V7.bed


*[[Media:ConvertProbesHg38_2_BedHg19.txt | ConvertProbesHg38_2_BedHg19.pl]]
*Convert from hg38 reference positions to hg19 reference (which RNA-Seq data was mapped to) using [http://genome.ucsc.edu/cgi-bin/hgLiftOver UCSC LiftOver]
**CA12k_Nov2014_V4.bed > CA12k_Nov2014_V4_hg19.bed
**CA12k_Nov2014_V7.bed > CA12k_Nov2014_V7_hg19.bed


===Bedtools Coverage with RNA-Seq Data===
===Bedtools Coverage with RNA-Seq Data===

Revision as of 06:52, 28 April 2015

Checking RNA-Seq Read Coverage of Probe Targets

Create BED File for Probe Targets

  • Convert from hg38 reference positions to hg19 reference (which RNA-Seq data was mapped to) using UCSC LiftOver
    • CA12k_Nov2014_V4.bed > CA12k_Nov2014_V4_hg19.bed
    • CA12k_Nov2014_V7.bed > CA12k_Nov2014_V7_hg19.bed

Bedtools Coverage with RNA-Seq Data

  • Workspace
    • genome-miner:/home/mzcai/CA12kNov2014_V4_CaptureAnalysis
    • genome-miner:/home/mzcai/CA12kNov2014_V7_CaptureAnalysis
  • RNA-Seq data from: /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR$
    • RL-BA8-sec9-t-N701-15May14_S1_mapped/RL-BA8-sec9-t-N701-15May14_S1_Aligned.sorted.bam
    • RL-BA8-sec9-n-N702-15May14_S2_mapped/RL-BA8-sec9-n-N702-15May14_S2_Aligned.sorted.bam
  • Commands
 /home/mzcai/softwares/bedtools-2.20.1/bin/coverageBed -hist -abam RL-BA8-sec9-t-N701-15May14_S1_mapped/RL-BA8-sec9-t-N701-15May14_S1_Aligned.sorted.bam -b CA12k_Nov2014_V4.bed >